I've never seen that happen.

It reminds me though of how "Preferences" always moves around. Some apps put it in Edit, others in Tools, some have their own Options menu... make up your damn minds.
Even worse than the hardcoded colours are those that try to look pretty (Office-style menus, basically all of KDE, most .Net apps) and either ignore user settings entirely (gah what is this brightly coloured window in my dark-themed environment) or create a horrid mash of user settings and their own styles. You can also see this on many web pages if you change the default background colour of your browser - don't even think of using black.
This extends beyond appearance. Try to use a GTK app in Windows and see how different everything behaves as well. They somehow managed to make the global Alt+Numpad shortcut not work. Or KDE in Xubuntu, where a single click selects items from a file selector where all other programs require a double click. (I actually prefer the double click, as I like to click in the list and navigate with the arrows, or see thumbnails, etc.)
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